TopPicProformaParser.GetIndexLookup still uses char.IsUpper to build residue indexes. ProFormaParser now accepts a caller-supplied residue validator, so TopPIC conversion can mis-index tags when a caller uses a non-standard residue alphabet.
Follow up by either adding equivalent validator configuration to TopPicProformaParser or explicitly documenting that it only supports the standard alphabet.
Related: #120
TopPicProformaParser.GetIndexLookupstill useschar.IsUpperto build residue indexes.ProFormaParsernow accepts a caller-supplied residue validator, so TopPIC conversion can mis-index tags when a caller uses a non-standard residue alphabet.Follow up by either adding equivalent validator configuration to
TopPicProformaParseror explicitly documenting that it only supports the standard alphabet.Related: #120